I take it TocFixer won't work on .cue/.iso with no .wav files.
There's a source for images that have all the games in that format. I tried playing Cosmic Fantasy 2 and the audio tracks are all out of wack.
I think you mean that they're in BIN/CUE format, if not, that was wrong of them to rename the BIN to ISO, but yeah, this is not a problem either.
1) Mount the CUE file with a virtual CD/DVD emulator like Alcohol 52%/Daemon Tools, etc.
2) Run TurboRip and point it to the virtual CD drive and rip it normally.
3) That'll yield you a full ISO/WAV/CUE image file set and then you can run TocFixer on it.
4) Burn the CUE file of that new image file set, and you're ready to go!
To be sure that the TOC is damaged, try using an emulator like MagicEngine and seeing if it detects the name of the game like I mentioned earlier. If it just shows you "PCECD" then in fact the TOC is altered due to MP3 encoding.
The history of the problems caused by MP3 encoding is because when you decode them back to a full WAV file, the original file size cannot be restored, it's close, but not exact. OGG solves this and if it had been used instead, all those problems would've been avoided. The only drawback is for us audiophiles that know some minor audio quality is lost with lossy encoding schemes such as MP3/OGG, but the amount of compression was too tempting and that's why they were used.